.coveragerc

-[run]
-branch = True
-omit =
-    */tests*
-    */__init__.py
-    q2_types/_version.py
-    versioneer.py
-
-[report]
-omit =
-    */tests*
-    */__init__.py
-    q2_types/_version.py
-    versioneer.py

.gitattributes

-q2_types/_version.py export-subst
+q2cli/_version.py export-subst

.github/ISSUE_TEMPLATE/6-where-to-go.md

@@ -59,6 +59,9 @@ Sorted alphabetically by repo name.
 - The q2-diversity plugin
   https://github.com/qiime2/q2-diversity/issues
 
+- The q2-diversity-lib plugin
+  https://github.com/qiime2/q2-diversity-lib/issues
+
 - The q2-emperor plugin
   https://github.com/qiime2/q2-emperor/issues
 

.github/SUPPORT.md

@@ -52,6 +52,8 @@ Sorted alphabetically by repo name.
   | The q2-demux plugin
 - [q2-diversity](https://github.com/qiime2/q2-diversity/issues)
   | The q2-diversity plugin
+- [q2-diversity-lib](https://github.com/qiime2/q2-diversity-lib/issues)
+  | The q2-diversity-lib plugin
 - [q2-emperor](https://github.com/qiime2/q2-emperor/issues)
   | The q2-emperor plugin
 - [q2-feature-classifier](https://github.com/qiime2/q2-feature-classifier/issues)

.gitignore

@@ -63,5 +63,3 @@ target/
 
 # vi
 .*.swp
-
-.DS_Store

.travis.yml

@@ -14,12 +14,12 @@ install:
   - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
   - conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml
   - source activate test-env
-  - conda install -q pytest-cov
-  - pip install -q flake8 coveralls
+  - conda install -q nose
+  - pip install -q flake8
   - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
   - make install
 script:
   - make lint
-  - make test-cov
-after_success:
-  - coveralls
+  - make test
+  - QIIMETEST= source tab-qiime
+  - QIIMETEST= qiime info

MANIFEST.in

 include versioneer.py
-include q2_types/_version.py
+include q2cli/_version.py

Makefile

-.PHONY: all lint test test-cov install dev clean distclean
+.PHONY: all lint test install dev clean distclean
 
 PYTHON ?= python
+PREFIX ?= $(CONDA_PREFIX)
 
 all: ;
 
@@ -9,16 +10,17 @@ lint:
 	flake8
 
 test: all
-	py.test
-
-test-cov: all
-	py.test --cov=q2_types
+	QIIMETEST= nosetests
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) setup.py install && \
+	mkdir -p $(PREFIX)/etc/conda/activate.d && \
+	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 dev: all
-	pip install -e .
+	pip install -e . && \
+	mkdir -p $(PREFIX)/etc/conda/activate.d && \
+	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 clean: distclean
 

README.md

-# q2-types
+# q2cli
+A [click-based](http://click.pocoo.org/) command line interface for [QIIME 2](https://github.com/qiime2/qiime2).
 
-[![Build Status](https://travis-ci.org/qiime2/q2-types.svg?branch=master)](https://travis-ci.org/qiime2/q2-types)
-[![Coverage Status](https://coveralls.io/repos/github/qiime2/q2-types/badge.svg?branch=master)](https://coveralls.io/github/qiime2/q2-types?branch=master)
+## Installation and getting help
 
-This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.
+Visit https://qiime2.org to learn more about q2cli and the QIIME 2 project.
+
+## Enabling tab completion
+
+### Bash
+
+To enable tab completion in Bash, run the following command or add it to your `.bashrc`/`.bash_profile`:
+
+```bash
+source tab-qiime
+```
+
+### ZSH
+
+To enable tab completion in ZSH, run the following commands or add them to your `.zshrc`:
+
+```bash
+autoload bashcompinit && bashcompinit && source tab-qiime
+```

bin/tab-qiime

+#!/usr/bin/env bash
+
+# Bash completion script that defers to a cached completion script representing
+# the state of the current QIIME 2 deployment.
+#
+# This script is intended to be executed on the command-line or in
+# .bashrc/.bash_profile:
+#
+#     source tab-qiime
+#
+
+_qiime_completion()
+{
+  # Attempt to find the cached completion script. If q2cli isn't installed, or
+  # is an incompatible version, don't attempt completion.
+  local completion_path="$(python -c "import q2cli.util; print(q2cli.util.get_completion_path())" 2> /dev/null)"
+
+  if [[ $? != 0 ]]; then
+    unset COMPREPLY
+    return 0
+  fi
+
+  # If the completion script exists, attempt completion by invoking the script
+  # in a subshell, supplying COMP_WORDS and COMP_CWORD. Capture the output as
+  # the completion reply. If the completion script failed, don't attempt
+  # completion.
+  if [[ -f "$completion_path" ]] ; then
+    COMPREPLY=( $(COMP_WORDS="${COMP_WORDS[*]}" COMP_CWORD="${COMP_CWORD}" "$completion_path" 2> /dev/null) )
+
+    if [[ $? != 0 ]]; then
+      unset COMPREPLY
+      return 0
+    fi
+  else
+    unset COMPREPLY
+    return 0
+  fi
+
+  return 0
+}
+
+# Enable default readline and bash completion behavior when `_qiime_completion`
+# doesn't have a reply.
+complete -F _qiime_completion -o default -o bashdefault qiime
+
+# Execute a `qiime` command (any command will do) so that tab-completion will
+# work out-of-the-box (e.g. with a fresh installation of q2cli). Running a
+# command will create or refresh the cache if necessary, which contains the
+# actual completion script.
+#
+# Ignore stdout to avoid displaying help text to users enabling tab-completion.
+# stderr displays the note about cache refreshing, as that can take a few
+# moments to complete.
+qiime > /dev/null

ci/recipe/conda_build_config.yaml

 python:
-   - 3.6
+  - 3.6

ci/recipe/meta.yaml

@@ -3,33 +3,34 @@
 {% set release = '.'.join(version.split('.')[:2]) %}
 
 package:
-  name: q2-types
+  name: q2cli
   version: {{ version }}
 
 source:
   path: ../..
+
 build:
   script: make install
+  entry_points:
+    - qiime=q2cli.__main__:qiime
 
 requirements:
   host:
-    - python {{ python }}
+    - python  {{ python }}
     - setuptools
 
   run:
-    - python {{ python }}
-    - scikit-bio >=0.5.4
-    # TODO: unset this pin once pandas 0.24.x is sorted out upstream
-    - pandas 0.23.4
-    - biom-format >=2.1.5,<2.2.0
-    - ijson
-    - h5py
+    - python  {{ python }}
+    - pip
+    - click
     - qiime2 {{ release }}.*
 
 test:
   imports:
-    - q2_types
-    - qiime2.plugins.types
+    - q2cli
+
+  commands:
+    - QIIMETEST= qiime --help
 
 about:
   home: https://qiime2.org

debian/changelog

+q2-types (2019.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Liubov Chuprikova <chuprikovalv@gmail.com>  Thu, 13 Jun 2019 22:21:11 +0200
+
 q2-types (2019.1.0-1) unstable; urgency=medium
 
   * Initial release (Closes: #925931)

hooks/50_activate_q2cli_tab_completion.sh

+if [ -n "${ZSH_VERSION-}" ]; then
+  autoload bashcompinit && bashcompinit && source tab-qiime
+elif [ -n "${BASH_VERSION-}" ]; then
+  source tab-qiime
+fi

q2_types/__init__.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import importlib
-
-from ._version import get_versions
-
-__version__ = get_versions()['version']
-del get_versions
-
-# feature_data needs to be imported before feature_table to avoid circular
-# import.
-importlib.import_module('q2_types.feature_data')
-importlib.import_module('q2_types.feature_table')
-importlib.import_module('q2_types.distance_matrix')
-importlib.import_module('q2_types.tree')
-importlib.import_module('q2_types.ordination')
-importlib.import_module('q2_types.sample_data')
-importlib.import_module('q2_types.per_sample_sequences')

q2_types/citations.bib

-@article{mcdonald2012biological,
-  title={The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome},
-  author={McDonald, Daniel and Clemente, Jose C and Kuczynski, Justin and Rideout, Jai Ram and Stombaugh, Jesse and Wendel, Doug and Wilke, Andreas and Huse, Susan and Hufnagle, John and Meyer, Folker and Knight, Rob and Caporaso, J Gregory},
-  journal={GigaScience},
-  volume={1},
-  number={1},
-  pages={7},
-  year={2012},
-  publisher={BioMed Central},
-  doi={10.1186/2047-217X-1-7}
-}
-
-@InProceedings{ mckinney-proc-scipy-2010,
-  author    = { Wes McKinney },
-  title     = { Data Structures for Statistical Computing in Python },
-  booktitle = { Proceedings of the 9th Python in Science Conference },
-  pages     = { 51 -- 56 },
-  year      = { 2010 },
-  editor    = { St{\'e}fan van der Walt and Jarrod Millman }
-}

q2_types/distance_matrix/__init__.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import importlib
-
-from ._format import LSMatFormat, DistanceMatrixDirectoryFormat
-from ._type import DistanceMatrix
-
-__all__ = ['LSMatFormat', 'DistanceMatrixDirectoryFormat', 'DistanceMatrix']
-
-importlib.import_module('q2_types.distance_matrix._transformer')

q2_types/distance_matrix/_format.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import skbio.io
-import qiime2.plugin.model as model
-
-from ..plugin_setup import plugin
-
-
-class LSMatFormat(model.TextFileFormat):
-    def sniff(self):
-        sniffer = skbio.io.io_registry.get_sniffer('lsmat')
-        return sniffer(str(self))[0]
-
-
-DistanceMatrixDirectoryFormat = model.SingleFileDirectoryFormat(
-    'DistanceMatrixDirectoryFormat', 'distance-matrix.tsv', LSMatFormat)
-
-
-plugin.register_formats(LSMatFormat, DistanceMatrixDirectoryFormat)

q2_types/distance_matrix/_transformer.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import skbio
-
-from ..plugin_setup import plugin
-from . import LSMatFormat
-
-
-@plugin.register_transformer
-def _1(data: skbio.DistanceMatrix) -> LSMatFormat:
-    ff = LSMatFormat()
-    with ff.open() as fh:
-        data.write(fh, format='lsmat')
-    return ff
-
-
-@plugin.register_transformer
-def _2(ff: LSMatFormat) -> skbio.DistanceMatrix:
-    return skbio.DistanceMatrix.read(str(ff), format='lsmat', verify=False)

q2_types/distance_matrix/_type.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-from qiime2.plugin import SemanticType
-
-from ..plugin_setup import plugin
-from . import DistanceMatrixDirectoryFormat
-
-
-DistanceMatrix = SemanticType('DistanceMatrix')
-
-plugin.register_semantic_types(DistanceMatrix)
-plugin.register_semantic_type_to_format(
-    DistanceMatrix,
-    artifact_format=DistanceMatrixDirectoryFormat
-)